### Abstract

Evaluating the Force Matrix constitutes the most computationally intensive part of a Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve the running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment. In this paper, we present a force matrix transformation that is capable of exploiting the symmetries in the force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The proposed transformation distributes the number oi interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. We also derive theoretical bounds for efficiency and load balance for prior work in the literature. We then prove some interesting and useful properties of our transformation and evaluate its advantages and disadvantages. A loop reordering optimization for the symmetric transformation is described, The performance of an MPI implementation of the transformation is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment.

Original language | English (US) |
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Title of host publication | High Performance Computing - HiPC 2007 - 14th International Conference, Proceedings |

Pages | 552-565 |

Number of pages | 14 |

State | Published - Dec 1 2007 |

Event | 14th International Conference on High-Performance Computing, HiPC 2007 - Goa, India Duration: Dec 18 2007 → Dec 21 2007 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 4873 LNCS |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Conference

Conference | 14th International Conference on High-Performance Computing, HiPC 2007 |
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Country | India |

City | Goa |

Period | 12/18/07 → 12/21/07 |

### Fingerprint

### ASJC Scopus subject areas

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*High Performance Computing - HiPC 2007 - 14th International Conference, Proceedings*(pp. 552-565). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4873 LNCS).

**A novel force matrix transformation with optimal load-balance for 3-body potential based parallel molecular dynamics using atom-decomposition in a heterogeneous cluster environment.** / Sumanth, J. V.; Swanson, David; Jiang, Hong.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*High Performance Computing - HiPC 2007 - 14th International Conference, Proceedings.*Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4873 LNCS, pp. 552-565, 14th International Conference on High-Performance Computing, HiPC 2007, Goa, India, 12/18/07.

}

TY - GEN

T1 - A novel force matrix transformation with optimal load-balance for 3-body potential based parallel molecular dynamics using atom-decomposition in a heterogeneous cluster environment

AU - Sumanth, J. V.

AU - Swanson, David

AU - Jiang, Hong

PY - 2007/12/1

Y1 - 2007/12/1

N2 - Evaluating the Force Matrix constitutes the most computationally intensive part of a Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve the running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment. In this paper, we present a force matrix transformation that is capable of exploiting the symmetries in the force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The proposed transformation distributes the number oi interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. We also derive theoretical bounds for efficiency and load balance for prior work in the literature. We then prove some interesting and useful properties of our transformation and evaluate its advantages and disadvantages. A loop reordering optimization for the symmetric transformation is described, The performance of an MPI implementation of the transformation is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment.

AB - Evaluating the Force Matrix constitutes the most computationally intensive part of a Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of the number of atoms in the system. Fortunately, there exist symmetries in the Force Matrix that can be exploited to improve the running time of the algorithm. While this optimization is straight forward to implement in the case of sequential code, it has proven to be nontrivial for parallel code even in a homogeneous environment. In this paper, we present a force matrix transformation that is capable of exploiting the symmetries in the force matrix in both a homogeneous and a heterogeneous environment while balancing the load among all the participating processors. The proposed transformation distributes the number oi interactions to be computed uniformly among all the slices of the force matrix along any of the axes. The transformed matrix can be scheduled using any well known heterogeneous slice-level scheduling technique. We also derive theoretical bounds for efficiency and load balance for prior work in the literature. We then prove some interesting and useful properties of our transformation and evaluate its advantages and disadvantages. A loop reordering optimization for the symmetric transformation is described, The performance of an MPI implementation of the transformation is studied in terms of the Step Time Variation Ratio (STVR) in a homogeneous and heterogeneous environment.

UR - http://www.scopus.com/inward/record.url?scp=38349062683&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=38349062683&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:38349062683

SN - 9783540772194

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 552

EP - 565

BT - High Performance Computing - HiPC 2007 - 14th International Conference, Proceedings

ER -